ClinVar: updates to support classifications of both germline and somatic variants.

ClinVar (www.ncbi.nlm.

Elucidating immunological characteristics of the adenoma-carcinoma sequence in colorectal cancer patients in South Korea using a bioinformatics approach.

Colorectal cancer (CRC) is one of the top five most common and life-threatening malignancies worldwide. Most CRC develops from advanced colorectal adenoma (ACA), a precancerous stage, through the adenoma-carcinoma sequence. However, its underlying mechanisms, including how the tumor microenvironment changes, remain elusive.

Prioritizing susceptibility genes for the prognosis of male-pattern baldness with transcriptome-wide association study.

Background: Male-pattern baldness (MPB) is the most common cause of hair loss in men. It can be categorized into three types: type 2 (T2), type 3 (T3), and type 4 (T4), with type 1 (T1) being considered normal. Although various MPB-associated genetic variants have been suggested, a comprehensive study for linking these variants to gene expression regulation has not been performed to the best of our knowledge.

Large-scale integrative analysis of juvenile idiopathic arthritis for new insight into its pathogenesis.

Background: Juvenile idiopathic arthritis (JIA) is one of the most prevalent rheumatic disorders in children and is classified as an autoimmune disease (AID). While a robust genetic contribution to JIA etiology has been established, the exact pathogenesis remains unclear.

Methods: To prioritize biologically interpretable susceptibility genes and proteins for JIA, we conducted transcriptome-wide and proteome-wide association studies (TWAS/PWAS).

Meta-analysis of single-cell RNA-sequencing data for depicting the transcriptomic landscape of chronic obstructive pulmonary disease.

Chronic obstructive pulmonary disease (COPD) is a respiratory disease characterized by airflow limitation and chronic inflammation of the lungs that is a leading cause of death worldwide. Since the complete pathological mechanisms at the single-cell level are not fully understood yet, an integrative approach to characterizing the single-cell-resolution landscape of COPD is required. To identify the cell types and mechanisms associated with the development of COPD, we conducted a meta-analysis using three single-cell RNA-sequencing datasets of COPD.

A Transcriptome-Wide Analysis of Psoriasis: Identifying the Potential Causal Genes and Drug Candidates.

Psoriasis is a chronic inflammatory skin disease characterized by cutaneous eruptions and pruritus. Because the genetic backgrounds of psoriasis are only partially revealed, an integrative and rigorous study is necessary. We conducted a transcriptome-wide association study (TWAS) with the new Genotype-Tissue Expression version 8 reference panels, including some tissue and multi-tissue panels that were not used previously.

An approach to studying a very rare neurodegenerative disease using a disease with higher prevalence with shared pathways and genes: Cerebral adrenoleukodystrophy and Alzheimer's disease.

Cerebral adrenoleukodystrophy (cALD) is a rare neurodegenerative disease characterized by inflammatory demyelination in the central nervous system. Another neurodegenerative disease with a high prevalence, Alzheimer's disease (AD), shares many common features with cALD such as cognitive impairment and the alleviation of symptoms by erucic acid. We investigated cALD and AD in parallel to study the shared pathological pathways between a rare disease and a more common disease.

A transcriptome-wide association study of uterine fibroids to identify potential genetic markers and toxic chemicals.

Uterine fibroid is one of the most prevalent benign tumors in women, with high socioeconomic costs. Although genome-wide association studies (GWAS) have identified several loci associated with uterine fibroid risks, they could not successfully interpret the biological effects of genomic variants at the gene expression levels. To prioritize uterine fibroid susceptibility genes that are biologically interpretable, we conducted a transcriptome-wide association study (TWAS) by integrating GWAS data of uterine fibroid and expression quantitative loci data.

Identifying novel antimicrobial peptides from venom gland of spider by deep multi-task learning.

Antimicrobial peptides (AMPs) show promises as valuable compounds for developing therapeutic agents to control the worldwide health threat posed by the increasing prevalence of antibiotic-resistant bacteria. Animal venom can be a useful source for screening AMPs due to its various bioactive components. Here, the deep learning model was developed to predict species-specific antimicrobial activity.

When function is biological: Discerning how silver nanoparticle structure dictates antimicrobial activity.

Silver nanomaterials have potent antibacterial properties that are the foundation for their wide commercial use as well as for concerns about their unintended environmental impact. The nanoparticles themselves are relatively biologically inert but they can undergo oxidative dissolution yielding toxic silver ions. A quantitative relationship between silver material structure and dissolution, and thus antimicrobial activity, has yet to be established.

Integrative transcriptome-wide analysis of atopic dermatitis for drug repositioning.

Atopic dermatitis (AD) is one of the most common inflammatory skin diseases, which significantly impact the quality of life. Transcriptome-wide association study (TWAS) was conducted to estimate both transcriptomic and genomic features of AD and detected significant associations between 31 expression quantitative loci and 25 genes. Our results replicated well-known genetic markers for AD, as well as 4 novel associated genes.

Identification of sp. nov., sp. nov. and sp. nov. and emended description of the genus .

Three chitinolytic, Gram-negative, light pink, capsule-forming, rod-shaped bacterial strains with gliding motion (MYSH2, MJ1a and dk17) were isolated from seashells, soil and foxtail, respectively. Phylogenetic analysis of the 16S rRNA gene sequences and concatenated alignment of 92 core genes indicated that strains MYSH2, MJ1a and dk17 were novel species of the genus and exhibited a high 16S rRNA sequence similarity (i.e.

sp. nov., a carotenoid-producing bacterium isolated from surface seawater.

A Gram-negative, moderately halophilic bacterium, designated as strain Y3S6, was isolated from a surface seawater sample collected from Dongangyoeng cave, Udo-myeon, Jeju-si, Jeju-do, Repulic of Korea. Cells of strain Y3S6 were aerobic, rod-shaped, non-sporulated, yellow, catalase- negative, oxidase-negative and motile with one polar flagellum. Growth of strain Y3S6 occurred at 15-40 °C (optimum: 25-30 °C), at pH 6.

Tear Neuromediators in Subjects with and without Dry Eye According to Ocular Sensitivity.

To investigate differences of tear neuromediators between subjects with and without dry eye (DE) depending on the ocular sensitivity. Thirty-one subjects with DE and 29 subjects without DE were recruited in this study. The eyes were stimulated by exposure to an irritating product applied to the periocular region.

sp. nov. and sp. nov., isolated from Jeongbang Waterfall on Jeju Island.

Two bacterial strains, designated MJB4 and SJ7, were isolated from water samples collected from Jeongbang Falls on Jeju Island, Republic of Korea. Phylogenetic analysis of 16S rRNA gene sequences indicated that the two strains belonged to the genera and , owing to their high similarities to DSM 29641 (97.5 %) and FA042 (96.

A Deep Learning Approach with Data Augmentation to Predict Novel Spider Neurotoxic Peptides.

As major components of spider venoms, neurotoxic peptides exhibit structural diversity, target specificity, and have great pharmaceutical potential. Deep learning may be an alternative to the laborious and time-consuming methods for identifying these peptides. However, the major hurdle in developing a deep learning model is the limited data on neurotoxic peptides.

sp. nov., a carotenoid and flexirubin-type pigment producing species isolated from flooded paddy field.

A Gram-stain-negative, aerobic, asporogenous, motile by gliding, dull-yellow, long rod-shaped bacterial strain, designated SNL9, was isolated from a flooded paddy field near Dongguk University, Republic of Korea. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that SNL9 represents a member of the genus and is most closely related to DS-12 (96.2%) and YIM 102796 (96.

An Integrative Transcriptomic Analysis of Systemic Juvenile Idiopathic Arthritis for Identifying Potential Genetic Markers and Drug Candidates.

Systemic juvenile idiopathic arthritis (sJIA) is a rare subtype of juvenile idiopathic arthritis, whose clinical features are systemic fever and rash accompanied by painful joints and inflammation. Even though sJIA has been reported to be an autoinflammatory disorder, its exact pathogenesis remains unclear. In this study, we integrated a meta-analysis with a weighted gene co-expression network analysis (WGCNA) using 5 microarray datasets and an RNA sequencing dataset to understand the interconnection of susceptibility genes for sJIA.

sp. nov., a fibrillar matrix-producing bacterium isolated from the rhizosphere of rice plant.

A novel fibrillar matrix-producing, rod-shaped, red-orange, asporogenous, aerobic bacterium, designated DK36, was isolated from roots of a rice plant in the Ilsan region near Dongguk University, South Korea. Cells of strain DK36 were Gram-stain-negative and motile by means of gliding. The temperature and pH ranges for growth were 7-35 °C (optimum: 30 °C) and pH 5-10 (optimum: pH 7.

Ovarian transcriptome profiles associated with sexual maturation in Pacific abalone (Haliotis discus hannai).

Background: There is now abundant information on genes involved in molluscan oogenesis and their associations with ovarian development. However, few studies have investigated the ovarian transcriptome of Pacific abalone (Haliotis discus hannai).

Objective: The objective of this study was to identify genes related to ovarian development and maturation in Pacific abalone utilizing RNA-sequencing (RNA-seq) and to verify the genes most relevant to different stages of maturation.

Antibacterial and Anti-Inflammatory Effects of Novel Peptide Toxin from the Spider .

The prevalence of antibiotic-resistant bacteria has become an immediate threat to public health. Antimicrobial peptides are attracting attention as a new source of antibiotics due to their ability to prevent drug-resistances with fewer side effects. Spider venom is composed of various bioactive substances with multiple functionalities such as antimicrobial and anti-inflammatory effects.

sp. nov., a gamma radiation-resistant bacterium isolated from gamma ray-irradiated soil.

A gamma radiation-resistant and pink-pigmented bacterial strain, designated as 17Sr1-39, was isolated from a gamma ray-irradiated soil sample collected in the Republic of Korea. Cells were Gram-stain-negative, strictly aerobic, flagellated, asporogenous, rod-shaped and methylotrophic. Results of 16S rRNA gene sequence analysis showed that strain 17Sr1-39 was phylogenetically related to PR1016A (97.

ClinVar: improvements to accessing data.

ClinVar is a freely available, public archive of human genetic variants and interpretations of their relationships to diseases and other conditions, maintained at the National Institutes of Health (NIH). Submitted interpretations of variants are aggregated and made available on the ClinVar website (https://www.ncbi.

Meta-Analysis of Polymyositis and Dermatomyositis Microarray Data Reveals Novel Genetic Biomarkers.

Polymyositis (PM) and dermatomyositis (DM) are both classified as idiopathic inflammatory myopathies. They share a few common characteristics such as inflammation and muscle weakness. Previous studies have indicated that these diseases present aspects of an auto-immune disorder; however, their exact pathogenesis is still unclear.